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Pennsylvania Station opened on September 15, 1911. It is the third railroad depot on its North Charles Street site. The first one was a wooden structure built by the Northern Central Railway that began operating in 1873. This was replaced in 1886 by the Charles Street Union Station, which featured a three-storybrick building situated below street level with a sloping driveway that led to its entrance and a train shed that measured 76 by 360 feet (23.16 by 109.73 meters).[3]

Penn Station is served by Amtrak, MARC, and the Maryland Transit Administration's light rail system. The station is the northern terminus of the Light Rail's Penn-Camden shuttle, connecting the Mount Vernon neighborhood with downtown; the southern terminus is Baltimore's Camden Station. MARC offers service between Washington, D.C., and Perryville. Amtrak Acela Express and Northeast Regional trains from Penn Station serve destinations along the Northeast Corridor between Boston and Washington, D.C. Some Regional trains from the station continue into Virginia and serve Alexandria, Newport News, Norfolk, Lynchburg, and points in between. Other long-distance trains from the station serve:

Before Amtrak's creation on May 1, 1971, Penn Station served as the main Baltimore station for its original owner, the Pennsylvania Railroad (PRR), though passenger trains of the Western Maryland Railway also used Penn Station as well. Until the late 1960s, the PRR also operated long-distance trains over its historic Northern Central Railway line from Penn Station to Harrisburg and beyond, such as "The General" to Chicago, the "Spirit of St. Louis" to its Missouri namesake, and the "Buffalo Day Express" and overnight "Northern Express" between Washington, DC, and Buffalo, New York. As late as 1956, this route also hosted the "Liberty Limited" to Chicago and the "Dominion Limited" to Toronto, Canada. The Baltimore Light Rail now operates over much of the Northern Central Railway's right of way in Baltimore and Baltimore County; however, the spur connecting Penn Station to this right of way is not the route originally taken by Northern Central trains. Baltimore Light Rail service began in 1997.

As part of the Northeast Corridor Improvement Project, the station was restored to its 1911 appearance in 1984.[4]

The station's use as a Western Maryland station stop allowed passengers from Penn Station to ride directly to various Maryland towns such as Westminster, Hagerstown, and Cumberland. Passenger service on the Western Maryland ended in 1958.

Baltimore Penn Station is also used for MARC train storage during the weekends and overnight via off-peak service times on tracks 1, 3, 5, and F.

In 2004, the City of Baltimore, through its public arts program, commissioned sculptor Jonathan Borofsky to create a sculpture as the centerpiece of a re-designed plaza in front of Penn Station. His work, a 51-foot (15.5 m)-tall aluminum statue entitled Male/Female, has generated considerable controversy ever since. Its defenders cite the contemporary imagery and artistic expression as complementing an urban landscape, while opponents criticize what they decry as a clash with Penn Station's Beaux-Arts architecture, detracting from its classic lines.

"Could this explain why defenders of "Male/Female", the sculpture in front of Penn Station, get so irritable? That large piece of quadrupedal artwork is out there all on its own, unclothed of commemorative armor that might deflect public criticism – unless you want to think of it as a memorial to the war between the sexes, but that's an issue that people tend to have a lot of different and strongly held opinions about anyway. No, "Male/Female" gets a lot of attention strictly on its artistic merits, and much of it isn't very positive, especially concerning its setting in front of the Beaux–Arts railroad station. This drives its proponents up the wall."

Three years later, Baltimore Sun columnist Dan Rodricks ridiculed the artwork, writing on August 26, 2007, "Patrons of art here paid $750,000 for a 51-foot sculpture...that looks like Gort from The Day the Earth Stood Still. I look at it and want to say: 'Klaatu barada nikto!' It's the first thing visitors see when they walk out of the train station."[6] Another Sun reporter, commenting in July 2008 on what she described as the "stormy relationship" between Baltimore and public art, said "People's hate for Penn Station's behemoth Male/Female sculpture has burned for years."[7]

It has also been featured a few times in the Zippycomic strip, beginning with the August 26, 2004 installment. Its cartoonistBill Griffith opined that "the sculpture as I look at it is both intriguing and compelling but also a little kitschy, and I like that. It's a nice place to be – high art and low art at the same time." He was also attracted to its message that people are full of contradictions and its provocativeness, stating that "you can't not react to it."[8][9]

Several proposals have been made to convert the upper floors of the station in a hotel. In 2001, an agreement was made with James M. Jost & Co. Inc. to convert the upper three floors into a 72-room hotel.[10] This project was never completed. The proposal resurfaced in 2006 with a new, unnamed developer.[11] This proposal was also never completed. In 2009, the idea surfaced once again as Amtrak announced it had reached an agreement with a developer for a 77-room hotel to be called The Inn at Penn Station.[12] This project was later reported as stalled along with many other hotel proposals in Baltimore.[13]

During what became known as the Checkers speech, on September 23, 1952, Richard Nixon, then a U.S. Senator from California and the Republican Party's nominee for Vice President, cited Penn Station as the place where a package was waiting for him, containing a cocker spaniel dog his daughter Tricia would name "Checkers." Nixon referred to the station by its former name, "Union Station in Baltimore."